Performance of marker-based relatedness estimators in natural populations of outbred vertebrates

Adoptions of unrelated infants in wild Taihangshan macaques (Macaca mulatta tcheliensis), Jiyuan, north China

Infant-care behavior, a range of caring behaviors by parental or alloparental individuals towards infants unable to live independently, plays a significant role in the survival of infants and the continuation of the species in non-human primates. During a behavioral ecological study of Taihangshan macaques, we observed 2 cases of infant adoptions by unrelated adult females. In case 1, a multiparous female adopted a lost infant from a neighboring group, with the infant being snatched back by her biological mother 35 days after the adoption. This is the first report of cross-group adoption in Maca ca. In case 2, a nulliparous adult female, who had been once adopted by her elder sister, adopted an orphan from her group for 36 days. We describe the details of adoptions in Taihangshan macaques and explore possible reasons for adoptions to contribute to understanding the evolution of infant-care behavior and altruistic behavior of adoption in primates.

Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of identical-by-descent DNA segments (IBD) yield the most precise relatedness estimates. Here, we leverage different methods for estimating IBD segments from low-depth whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4 to 6× depth data from a rhesus macaque (Macaca mulatta) population with long-term pedigree data, we show that we can infer the number and length of IBD segments across the genome with high accuracy even at 0.5× sequencing depth. In line with expectations based on simulation, the resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. By comparing the IBD-based estimates with pedigree and short tandem repeat-based methods, we show that IBD estimates are more reliable and provide more detailed information on kinship. The inferred IBD segments also identify cryptic genetic relatives not represented in the pedigree and reveal elevated recombination rates in females relative to males, which enables the majority of close maternal and paternal kin to be distinguished with genotype data alone. Our findings represent a breakthrough in the ability to study the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.

Assessing the suitability of a one-time sampling event for close-kin mark-recapture: A caribou case study

Abundance estimation is frequently an objective of conservation and monitoring initiatives for threatened and other managed populations. While abundance estimation via capture-mark-recapture or spatially explicit capture-recapture is now common, such approaches are logistically challenging and expensive for species such as boreal caribou (Rangifer tarandus), which inhabit remote regions, are widely dispersed, and exist at low densities. Fortunately, the recently developed 'close-kin mark-recapture' (CKMR) framework, which uses the number of kin pairs obtained within a sample to generate an abundance estimate, eliminates the need for multiple sampling events. As a result, some caribou managers are interested in using this method to generate an abundance estimate from a single, non-invasive sampling event for caribou populations. We conducted a simulation study using realistic boreal caribou demographic rates and population sizes to assess how population size and the proportion of the population surveyed impact the accuracy and precision of single-survey CKMR-based abundance estimates. Our results indicated that abundance estimates were biased and highly imprecise when very small proportions of the population were sampled, regardless of the population size. However, the larger the population size, the smaller the required proportion of the population surveyed to generate both accurate and reasonably precise estimates. Additionally, we also present a case study in which we used the CKMR framework to generate annual female abundance estimates for a small caribou population in Jasper National Park, Alberta, Canada, from 2006 to 2015 and compared them to existing published capture-mark-recapture-based estimates. Both the accuracy and precision of the annual CKMR-based abundance estimates varied across years and were sensitive to the proportion of pairwise kinship comparisons which yielded a mother-offspring pair. Taken together, our study demonstrates that it is possible to generate CKMR-based abundance estimates from a single sampling event for small caribou populations, so long as a sufficient sampling intensity can be achieved.

Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness. Here, we leverage novel methods for estimating locus-specific IBD from low coverage whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4-6× coverage data from a rhesus macaque (Macaca mulatta) population with available long-term pedigree data, we show that we can call the number and length of IBD segments across the genome with high accuracy even at 0.5× coverage. The resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. They identify cryptic genetic relatives that are not represented in the pedigree and reveal elevated recombination rates in females relative to males, which allows us to discriminate maternal and paternal kin using genotype data alone. Our findings represent a breakthrough in the ability to understand the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.

Female chimpanzees avoid inbreeding even in the presence of substantial bisexual philopatry

Inbreeding (reproduction between relatives) often decreases the fitness of offspring and is thus expected to lead to the evolution of inbreeding avoidance strategies. Chimpanzees (Pan troglodytes) are expected to avoid inbreeding as they are long-lived, invest heavily in offspring and may encounter adult, opposite sex kin frequently, especially in populations where both males and females commonly remain in the group in which they were born (bisexual philopatry). However, it is unclear whether substantial bisexual philopatry has been a feature of chimpanzees' evolutionary history or whether it is a result of recent anthropogenic interference, as the only groups for which it has been documented are significantly impacted by human encroachment and experience notable rates of potentially unsustainable inbreeding. Here we use 14 years of observational data and a large genomic dataset of 256 481 loci sequenced from 459 individuals to document dispersal and inbreeding dynamics in an eastern chimpanzee (P. t. schweinfurthii) community with low levels of anthropogenic disturbance. We document the first case of substantial bisexual philopatry in a relatively undisturbed chimpanzee community and show that, despite an increased inbreeding risk incurred by females who do not disperse before reaching reproductive age, natal females were still able to avoid producing inbred offspring.

Kinship composition in mammals

Understanding the evolution of group-living and cooperation requires information on who animals live and cooperate with. Animals can live with kin, non-kin or both, and kinship structure can influence the benefits and costs of group-living and the evolution of within-group cooperation. One aspect of kinship structure is kinship composition, i.e. a group-level attribute of the presence of kin and/or non-kin dyads in groups. Despite its putative importance, the kinship composition of mammalian groups has yet to be characterized. Here, we use the published literature to build an initial kinship composition dataset in mammals, laying the groundwork for future work in the field. In roughly half of the 18 species in our sample, individuals lived solely with same-sex kin, and, in the other half, individuals lived with related and unrelated individuals of the same sex. These initial results suggest that it is not rare for social mammals to live with unrelated individuals of the same sex, highlighting the importance of considering indirect and direct fitness benefits as co-drivers of the evolution of sociality. We hope that our initial dataset and insights will spur the study of kinship structure and sociality towards new exciting avenues.

Sex ratio and relatedness in the Griffon vulture (Gyps fulvus) population of Serbia

Background

Once a widespread species across the region of Southeast Europe, the Griffon vulture is now confined to small and isolated populations across the Balkan Peninsula. The population from Serbia represents its biggest and most viable population that can serve as an important reservoir of genetic diversity from which the birds can be used for the region's reintroduction programmes. The available genetic data for this valuable population are scarce and as a protected species that belongs to the highly endangered vulture group, it needs to be well described so that it can be properly managed and used as a restocking population. Considering the serious recent bottleneck event that the Griffon vulture population from Serbia experienced we estimated the overall relatedness among the birds from this population. Sex ratio, another important parameter that shows the vitality and strength of the population was evaluated as well.

Methods

During the annual monitoring that was performed in the period from 2013-2021, we collected blood samples from individual birds that were marked in the nests. In total, 169 samples were collected and each was used for molecular sexing while 58 presumably unrelated birds from different nests were used for inbreeding and relatedness analyses. The relatedness was estimated using both biparentally (10 microsatellite loci) and uniparentally (Cytb and D-loop I of mitochondrial DNA) inherited markers.

Results

The level of inbreeding was relatively high and on average it was 8.3% while the mean number of relatives for each bird was close to three. The sex ratio was close to 1:1 and for the analysed period of 9 years, it didn't demonstrate a statistically significant deviation from the expected ratio of 1:1, suggesting that this is a stable and healthy population. Our data suggest that, even though a relatively high level of inbreeding can be detected among the individual birds, the Griffon vulture population from Serbia can be used as a source population for restocking and reintroduction programmes in the region. These data combined with previously observed genetic differentiation between the populations from the Iberian and Balkan Peninsulas suggest that the introduction of foreign birds should be avoided and that local birds should be used instead.

Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (R_xy ), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (R_AB ), allele-sharing co-ancestry (AS)) across five species bred in captivity-including three birds and two mammals-with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using R_xy , R_AB , and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either R_xy or R_AB . Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.

Patterns of sex-biased dispersal are consistent with social and ecological constraints in a group-living cichlid fish

BACKGROUND

Sex-biased dispersal is a common and widespread phenomenon that can fundamentally shape the genetic structure of the social environments in which animals live. For animals that live in and move between social groups, sex-biased dispersal can result in an asymmetry in the degree of relatedness among cohabiting males and females, which can have strong implications for their social evolution. In this study, we measured the relatedness structure within and across groups of a wild population of Neolamprologus multifasciatus, a highly-social, shell-dwelling cichlid fish endemic to Lake Tanganyika, East Africa. In total, we genotyped 812 fish from 128 social groups at 20 microsatellite loci. Neolamprologus multifasciatus live at high densities, and also experience strong ecological constraints on free movement throughout their habitat. At the same time, they exhibit sex differences in the degree of reproductive competition within their groups and this makes them an excellent model system for studying the factors associated with sex-biased dispersal.

RESULTS

Social groups of N. multifasciatus consist of multiple males and females living together. We found that cohabiting females were unrelated to one another (Lynch-Ritland estimates of relatedness = 0.045 ± 0.15, average ± SD), while males shared much higher, albeit variable, levels of relatedness to other males in their groups (0.23 ± 0.27). We uncovered a pronounced decline in relatedness between males living in separate groups as the spatial separation between them increased, a pattern that was not evident in females. Female dispersal was also markedly constrained by the distribution and availability of nearby territories to which they could emigrate.

CONCLUSIONS

Our results indicate female-biased dispersal in N. multifasciatus. Our study also highlights how the spatial distribution of suitable dispersal destinations can influence the movement decisions of animals. We also emphasize how sex-biased dispersal can influence the relatedness structure of the social environment in which individuals interact and compete with one another.

Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation

Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non-random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150-160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (Melospiza melodia) population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant-native, native-native and immigrant-immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants' offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non-random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.

No evidence for female kin association, indications for extragroup paternity, and sex-biased dispersal patterns in wild western gorillas

Characterizing animal dispersal patterns and the rational behind individuals' transfer choices is a long-standing question of interest in evolutionary biology. In wild western gorillas (Gorilla gorilla), a one-male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher-than-expected within-group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extragroup paternity, we analyzed long-term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extragroup males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extragroup paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using R ST statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups.

Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore

Harvest can disrupt wildlife populations by removing adults with naturally high survival. This can reshape sociospatial structure, genetic composition, fitness, and potentially affect evolution. Genetic tools can detect changes in local, fine-scale genetic structure (FGS) and assess the interplay between harvest-caused social and FGS in populations. We used data on 1614 brown bears, Ursus arctos, genotyped with 16 microsatellites, to investigate whether harvest intensity (mean low: 0.13 from 1990 to 2005, mean high: 0.28 from 2006 to 2011) caused changes in FGS among matrilines (8 matrilines; 109 females ≥4 years of age), sex-specific survival and putative dispersal distances, female spatial genetic autocorrelation, matriline persistence, and male mating patterns. Increased harvest decreased FGS of matrilines. Female dispersal distances decreased, and male reproductive success was redistributed more evenly. Adult males had lower survival during high harvest, suggesting that higher male turnover caused this redistribution and helped explain decreased structure among matrilines, despite shorter female dispersal distances. Adult female survival and survival probability of both mother and daughter were lower during high harvest, indicating that matriline persistence was also lower. Our findings indicate a crucial role of regulated harvest in shaping populations, decreasing differences among "groups," even for solitary-living species, and potentially altering the evolutionary trajectory of wild populations.

Genetic relatedness in social groups of the emerald coral goby Paragobiodon xanthosoma creates potential for weak kin selection

Animals forming social groups that include breeders and nonbreeders present evolutionary paradoxes; why do breeders tolerate nonbreeders? And why do nonbreeders tolerate their situation? Both paradoxes are often explained with kin selection. Kin selection is, however, assumed to play little or no role in social group formation of marine organisms with dispersive larval phases. Yet, in some marine organisms, recent evidence suggests small-scale patterns of relatedness, meaning that this assumption must always be tested. Here, we investigated the genetic relatedness of social groups of the emerald coral goby, Paragobiodon xanthosoma. We genotyped 73 individuals from 16 groups in Kimbe Bay, Papua New Guinea, at 20 microsatellite loci and estimated pairwise relatedness among all individuals. We found that estimated pairwise relatedness among individuals within groups was significantly higher than the pairwise relatedness among individuals from the same reef, and pairwise relatedness among individuals from the same reef was significantly higher than the pairwise relatedness among individuals from different reefs. This spatial signature suggests that there may be very limited dispersal in this species. The slightly positive relatedness within groups creates the potential for weak kin selection, which may help to resolve the paradox of why breeders tolerate subordinates in P. xanthosoma. The other paradox, why nonbreeders tolerate their situation, is better explained by alternative hypotheses such as territory inheritance, and ecological and social constraints. We show that even in marine animals with dispersive larval phases, kin selection needs to be considered to explain the evolution of complex social groups.

Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.

How does contemporary selection shape oak phenotypes?

Most existing forests are subjected to natural and human-mediated selection pressures, which have increased due to climate change and the increasing needs of human societies for wood, fibre and fuel resources. It remains largely unknown how these pressures trigger evolutionary changes. We address this issue here for temperate European oaks (Quercus petraea and Q. robur), which grow in mixed stands, under even-aged management regimes. We screened numerous functional traits for univariate selection gradients and for expected and observed genetic changes over two successive generations. In both species, growth, leaf morphology and physiology, and defence-related traits displayed significant selection gradients and predicted shifts, whereas phenology, water metabolism, structure and resilience-related traits did not. However, the direction of the selection response and the potential for adaptive evolution differed between the two species. Quercus petraea had a much larger phenotypic and genetic variance of fitness than Q. robur. This difference raises concerns about the adaptive response of Q. robur to contemporary selection pressures. Our investigations suggest that Q. robur will probably decline steadily, particularly in mixed stands with Q. petraea, consistent with the contrasting demographic dynamics of the two species.

Opinion: Is gene mapping in wild populations useful for understanding and predicting adaptation to global change?

Changing environmental conditions will inevitably alter selection pressures. Over the long term, populations have to adapt to these altered conditions by evolutionary change to avoid extinction. Quantifying the 'evolutionary potential' of populations to predict whether they will be able to adapt fast enough to forecasted changes is crucial to fully assess the threat for biodiversity posed by climate change. Technological advances in sequencing and high-throughput genotyping have now made genomic studies possible in a wide range of species. Such studies, in theory, allow an unprecedented understanding of the genomics of ecologically relevant traits and thereby a detailed assessment of the population's evolutionary potential. Aimed at a wider audience than only evolutionary geneticists, this paper gives an overview of how gene-mapping studies have contributed to our understanding and prediction of evolutionary adaptations to climate change, identifies potential reasons why their contribution to understanding adaptation to climate change may remain limited, and highlights approaches to study and predict climate change adaptation that may be more promising, at least in the medium term.

Why don’t long-finned pilot whales have a widespread postreproductive lifespan? Insights from genetic data

In a handful of mammals, females show an extended postreproductive lifespan (PRLS), leading to questions over why they spend a substantial portion of their lifespan nonreproductive. Theoretical and empirical studies suggest that PRLS may evolve when 1) demographic patterns lead to increasing local relatedness as females age, and 2) females come into reproductive competition with their daughters, as these conditions lead to high relative benefits of helping kin versus reproducing in later life. However, evolutionary pathways to PRLS are poorly understood and empirical studies are scarce. Here, we use a dataset of 1522 individuals comprising 22 pods to investigate patterns of reproduction and relatedness in long-finned pilot whales Globicephala melas; a toothed whale without species-wide PRLS. We find a similar relatedness structure to whales with PRLS: pods appear composed of related matrilines, and relatedness of females to their pod increases with age, suggesting that this species could benefit from late-life help. Furthermore, females with a large number of philopatric adult daughters are less likely to reproduce, implying intergenerational reproductive competition between females. This suggests that individuals may display a plastic cessation of reproduction, switching to investing in existing offspring when they come into competition with their daughters. To the best of our knowledge, this is the first time such a relationship has been described in relation to PRLS, and it raises questions about whether this represents a step towards evolving PRLS or is a stable alternative strategy to widespread postreproductive periods.

Genetic homogeneity in the face of morphological heterogeneity in the harbor porpoise from the Black Sea and adjacent waters (Phocoena phocoena relicta)

Absence of genetic differentiation is usually taken as an evidence of panmixia, but can also reflect other situations, including even nearly complete demographic independence among large-sized populations. Deciphering which situation applies has major practical implications (e.g., in conservation biology). The endangered harbor porpoises in the Black Sea illustrates this point well. While morphological heterogeneity suggested that population differentiation may exist between individuals from the Black and Azov seas, no genetic study provided conclusive evidence or covered the entire subspecies range. Here, we assessed the genetic structure at ten microsatellite loci and a 3904 base-pairs mitochondrial fragment in 144 porpoises across the subspecies range (i.e., Aegean, Marmara, Black, and Azov seas). Analyses of the genetic structure, including FST, Bayesian clustering, and multivariate analyses revealed a nearly complete genetic homogeneity. Power analyses rejected the possibility of underpowered analyses (power to detect FST ≥ 0.008 at microsatellite loci). Simulations under various demographic models, evaluating the evolution of FST, showed that a time-lag effect between demographic and genetic subdivision is also unlikely. With a realistic effective population size of 1000 individuals, the expected "gray zone" would be at most 20 generations under moderate levels of gene flow (≤10 migrants per generation). After excluding alternative hypotheses, panmixia remains the most likely hypothesis explaining the genetic homogeneity in the Black Sea porpoises. Morphological heterogeneity may thus reflect other processes than population subdivision (e.g., plasticity, selection). This study illustrates how combining empirical and theoretical approaches can contribute to understanding patterns of weak population structure in highly mobile marine species.

Affiliation history and age similarity predict alliance formation in adult male bottlenose dolphins

Male alliances are an intriguing phenomenon in the context of reproduction since, in most taxa, males compete over an indivisible resource, female fertilization. Adult male bottlenose dolphins (Tursiops aduncus) in Shark Bay, Western Australia, form long-term, multilevel alliances to sequester estrus females. These alliances are therefore critical to male reproductive success. Yet, the long-term processes leading to the formation of such complex social bonds are still poorly understood. To identify the criteria by which male dolphins form social bonds with other males, we adopted a long-term approach by investigating the ontogeny of alliance formation. We followed the individual careers of 59 males for 14 years while they transitioned from adolescence (8-14 years of age) to adulthood (15-21 years old). Analyzing their genetic relationships and social associations in both age groups, we found that the vast majority of social bonds present in adolescence persisted through time. Male associations in early life predict alliance partners as adults. Kinship patterns explained associations during adolescence but not during adulthood. Instead, adult males associated with males of similar age. Our findings suggest that social bonds among peers, rather than kinship, play a central role in the development of adult male polyadic cooperation in dolphins.

Differences in MHC-B diversity and KIR epitopes in two populations of wild chimpanzees

The major histocompatibility complex (MHC) class I genes play a critical role within the immune system, both by the presentation of antigens from intracellular pathogens to immunocompetent cells and by the interaction with killer cell immunoglobulin-like receptors (KIR) on natural killer cells (NK cells). Genes of the MHC are highly diverse, and MHC variation can have effects on the immune functionality of individuals; hence, comparisons of MHC diversity among closely related phylogenetic taxa may give insight into the factors responsible for the shaping of its diversity. The four geographically separated chimpanzee subspecies differ in their overall genetic diversity, have different population histories, and are confronted with different pathogens in their natural habitat, all of which may affect MHC class I DNA sequence diversity. Here, we compare the MHC-B exon two DNA sequence diversity from 24 wild western and 46 wild eastern chimpanzees using necropsy and noninvasively collected fecal samples, respectively. We found a higher MHC-B exon two nucleotide diversity, in our western than eastern chimpanzees. The inclusion of previously published MHC-B exon two data from other western and eastern chimpanzees supported this finding. In addition, our results confirm and extend the finding of a very low C1 epitope frequency at eastern chimpanzee MHC-B molecules, which likely affects the ability of these molecules to interact with NK cells. While the understanding of the differing pathogen environments encountered by disparate populations of a species is a challenging endeavor, these findings highlight the potential for these pathogens to selectively shape immune system variation.

A Weighted Genomic Relationship Matrix Based on Fixation Index (FST) Prioritized SNPs for Genomic Selection

A dramatic increase in the density of marker panels has been expected to increase the accuracy of genomic selection (GS), unfortunately, little to no improvement has been observed. By including all variants in the association model, the dimensionality of the problem should be dramatically increased, and it could undoubtedly reduce the statistical power. Using all Single nucleotide polymorphisms (SNPs) to compute the genomic relationship matrix (G) does not necessarily increase accuracy as the additive relationships can be accurately estimated using a much smaller number of markers. Due to these limitations, variant prioritization has become a necessity to improve accuracy. The fixation index (F_ST) as a measure of population differentiation has been used to identify genome segments and variants under selection pressure. Using prioritized variants has increased the accuracy of GS. Additionally, F_ST can be used to weight the relative contribution of prioritized SNPs in computing G. In this study, relative weights based on F_ST scores were developed and incorporated into the calculation of G and their impact on the estimation of variance components and accuracy was assessed. The results showed that prioritizing SNPs based on their F_ST scores resulted in an increase in the genetic similarity between training and validation animals and improved the accuracy of GS by more than 5%.

Heritability of Horn Size in Thinhorn Sheep

Understanding the genetic basis of fitness-related trait variation has long been of great interest to evolutionary biologists. Secondary sexual characteristics, such as horns in bovids, are particularly intriguing since they can be potentially affected by both natural and sexual selection. Until recently, however, the study of fitness-related quantitative trait variation in wild species has been hampered by a lack of genomic resources, pedigree, and/or phenotype data. Recent innovations in genomic technologies have enabled wildlife researchers to perform marker-based relatedness estimation and acquire adequate loci density, enabling both the “top-down” approach of quantitative genetics and the “bottom-up” approach of association studies to describe the genetic basis of fitness-related traits. Here we combine a cross species application of the OvineHD BeadChip and horn measurements (horn length, base circumference, and volume) from harvested thinhorn sheep to examine the heritability and to perform a genome-wide single-nucleotide polymorphism association study of horn size in the species. Thinhorn sheep are mountain ungulates that reside in the mountainous regions of northwestern North America. Thinhorn sheep males grow massive horns that determine the social rank and mating success. We found horn length, base circumference, and volume to be moderately heritable and two loci to be suggestively associated with horn length.

Quality and quantity of genetic relatedness data affect the analysis of social structure

Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species' or population's mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioural study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4,235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses.

Genetic evaluation of the Iberian lynx ex situ conservation programme

Ex situ programmes have become critical for improving the conservation of many threatened species, as they establish backup populations and provide individuals for reintroduction and reinforcement of wild populations. The Iberian lynx was considered the most threatened felid species in the world in the wake of a dramatic decline during the second half of the 20th century that reduced its numbers to around only 100 individuals. An ex situ conservation programme was established in 2003 with individuals from the two well-differentiated, remnant populations, with great success from a demographic point of view. Here, we evaluate the genetic status of the Iberian lynx captive population based on molecular data from 36 microsatellites, including patterns of relatedness and representativeness of the two remnant genetic backgrounds among founders, the evolution of diversity and inbreeding over the years, and genetic differentiation among breeding facilities. In general terms, the ex situ population harbours most of the genetic variability found in the two wild populations and has been able to maintain reasonably low levels of inbreeding and high diversity, thus validating the applied management measures and potentially representing a model for other species in need of conservation.

Genomic selection on breeding time in a wild bird population

Artificial selection experiments are a powerful tool in evolutionary biology. Selecting individuals based on multimarker genotypes (genomic selection) has several advantages over phenotype-based selection but has, so far, seen very limited use outside animal and plant breeding. Genomic selection depends on the markers tagging the causal loci that underlie the selected trait. Because the number of necessary markers depends, among other factors, on effective population size, genomic selection may be in practice not feasible in wild populations as most wild populations have much higher effective population sizes than domesticated populations. However, the current possibilities of cost-effective high-throughput genotyping could overcome this limitation and thereby make it possible to apply genomic selection also in wild populations. Using a unique dataset of about 2000 wild great tits (Parus major), a small passerine bird, genotyped on a 650 k SNP chip we calculated genomic breeding values for egg-laying date using the so-called GBLUP approach. In this approach, the pedigree-based relatedness matrix of an "animal model," a special form of the mixed model, is replaced by a marker-based relatedness matrix. Using the marker-based relatedness matrix, the model seemed better able to disentangle genetic and permanent environmental effects. We calculated the accuracy of genomic breeding values by correlating them to the phenotypes of individuals whose phenotypes were excluded from the analysis when estimating the genomic breeding values. The obtained accuracy was about 0.20, with very little effect of the used genomic relatedness estimator but a strong effect of the number of SNPs. The obtained accuracy is lower than typically seen in domesticated species but considerable for a trait with low heritability (∼0.2) as avian breeding time. Our results show that genomic selection is possible also in wild populations with potentially many applications, which we discuss here.

Increasing accuracy of genomic selection in presence of high density marker panels through the prioritization of relevant polymorphisms

BACKGROUND

It becomes clear that the increase in the density of marker panels and even the use of sequence data didn't result in any meaningful increase in the accuracy of genomic selection (GS) using either regression (RM) or variance component (VC) approaches. This is in part due to the limitations of current methods. Association model are well over-parameterized and suffer from severe co-linearity and lack of statistical power. Even when the variant effects are not directly estimated using VC based approaches, the genomic relationships didn't improve after the marker density exceeded a certain threshold. SNP prioritization-based fixation index (F_ST) scores were used to track the majority of significant QTL and to reduce the dimensionality of the association model.

RESULTS

Two populations with average LD between adjacent markers of 0.3 (P1) and 0.7 (P2) were simulated. In both populations, the genomic data consisted of 400 K SNP markers distributed on 10 chromosomes. The density of simulated genomic data mimics roughly 1.2 million SNP markers in the bovine genome. The genomic relationship matrix (G) was calculated for each set of selected SNPs based on their F_ST score and similar numbers of SNPs were selected randomly for comparison. Using all 400 K SNPs, 46% of the off-diagonal elements (OD) were between - 0.01 and 0.01. The same portion was 31, 23 and 16% when 80 K, 40 K and 20 K SNPs were selected based on F_ST scores. For randomly selected 20 K SNP subsets, around 33% of the OD fell within the same range. Genomic similarity computed using SNPs selected based on F_ST scores was always higher than using the same number of SNPs selected randomly. Maximum accuracies of 0.741 and 0.828 were achieved when 20 and 10 K SNPs were selected based on F_ST scores in P₁ and P₂, respectively.

CONCLUSIONS

Genomic similarity could be maximized by the decrease in the number of selected SNPs, but it also leads to a decrease in the percentage of genetic variation explained by the selected markers. Finding the balance between these two parameters could optimize the accuracy of GS in the presence of high density marker panels.

Phenological mismatch drives selection on elevation, but not on slope, of breeding time plasticity in a wild songbird

Phenotypic plasticity is an important mechanism for populations to respond to fluctuating environments, yet may be insufficient to adapt to a directionally changing environment. To study whether plasticity can evolve under current climate change, we quantified selection and genetic variation in both the elevation (RNE ) and slope (RNS ) of the breeding time reaction norm in a long-term (1973-2016) study population of great tits (Parus major). The optimal RNE (the caterpillar biomass peak date regressed against the temperature used as cue by great tits) changed over time, whereas the optimal RNS did not. Concordantly, we found strong directional selection on RNE , but not RNS , of egg-laying date in the second third of the study period; this selection subsequently waned, potentially due to increased between-year variability in optimal laying dates. We found individual and additive genetic variation in RNE but, contrary to previous studies on our population, not in RNS . The predicted and observed evolutionary change in RNE was, however, marginal, due to low heritability and the sex limitation of laying date. We conclude that adaptation to climate change can only occur via micro-evolution of RNE, but this will necessarily be slow and potentially hampered by increased variability in phenotypic optima.

Inclusive fitness benefits mitigate costs of cuckoldry to socially paired males

Background

In socially monogamous species, reproduction is not always confined to paired males and females. Extra-pair males commonly also reproduce with paired females, which is traditionally thought to be costly to the females’ social partners. However, we suggest that when the relatedness between reproducing individuals is considered, cuckolded males can suffer lower fitness losses than otherwise expected, especially when the rate of cuckoldry is high. We combine theoretical modeling with a detailed genetic study on a socially monogamous wild fish, Variabilichromis moorii, which displays biparental care despite exceptionally high rates of extra-pair paternity.

Results

We measured the relatedness between all parties involved in V. moorii spawning events (i.e. between males and females in social pairs, females and their extra-pair partners, and paired males and their cuckolders), and we reveal that males are on average more related to their cuckolders than expected by chance. Queller–Goodnight estimates of relatedness between males and their cuckolders are on average r = 0.038 but can range up to r = 0.64. This also increases the relatedness between males and the extra-pair offspring under their care. These intriguing results are consistent with the predictions of our mathematical model, which shows that elevated relatedness between paired males and their cuckolders can be adaptive for both parties when competition for fertilizations is strong.

Conclusions

Our results show how cuckoldry by relatives can offset males’ direct fitness losses with inclusive fitness gains, which can be substantial in systems where males face almost certain paternity losses.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0620-6) contains supplementary material, which is available to authorized users.

Estimating selection on the act of inbreeding in a population with strong inbreeding depression

Inbreeding depression is widely regarded as a driving force in the evolution of dispersal, mate choice and sperm selection. However, due to likely costs of inbreeding avoidance, which are poorly understood, it is unclear to what extent selection to avoid inbreeding is expected in nature. Moreover, there are currently very few empirical estimates of the strength of selection against the act of inbreeding (mating with a relative), as opposed to the fitness costs of being inbred. Here, we use data from the individual-based study of red deer on the Scottish island of Rum, a strongly polygynous system which harbours a large inbreeding load, to estimate selection against the act of inbreeding for each sex. We use pedigree and genomic estimates of relatedness between individuals and measure fitness using both lifetime breeding success (number of calves born) and lifetime reproductive success (number of calves surviving to independence), with the latter incorporating inbreeding depression in calf survival. We find for both sexes that the repeatability of the act of inbreeding was low (< 0.1), suggesting little among-individual variation for this trait on which selection can act. Using the genomic measures, there was significant selection against the act of inbreeding in males, but not in females, and there was considerable uncertainty in the estimate in both sexes. We discuss possible explanations for these patterns and their implications for understanding the evolution of inbreeding avoidance in natural populations.

Use of molecular data in zoo and aquarium collection management: Benefits, challenges, and best practices

The global zoo and aquarium community widely recognizes that its animal collections and cooperative breeding programs are facing a sustainability crisis. It has become commonly accepted that numerous priority species cannot be maintained unless new management strategies are adopted. While molecular data have the potential to greatly improve management across a range of scenarios, they have been generally underutilized by the zoo and aquarium community. This failure to effectively apply molecular data to collection management has been due, in part, to a paucity of resources within the community on which to base informed decisions about when the use of such data is appropriate and what steps are necessary to successfully integrate data into management. Here, we identify three broad areas of inquiry where molecular data can inform management: 1) taxonomic identification; 2) incomplete or unknown pedigrees; and 3) hereditary disease. Across these topics, we offer a discussion of the advantages, limitations, and considerations for applying molecular data to ex situ animal populations in a style accessible to zoo and aquarium professionals. Ultimately, we intend for this compiled information to serve as a resource for the community to help ensure that molecular projects directly and effectively benefit the long-term persistence of ex situ populations.

How to estimate kinship

The concept of kinship permeates many domains of fundamental and applied biology ranging from social evolution to conservation science to quantitative and human genetics. Until recently, pedigrees were the gold standard to infer kinship, but the advent of next‐generation sequencing and the availability of dense genetic markers in many species make it a good time to (re)evaluate the usefulness of genetic markers in this context. Using three published data sets where both pedigrees and markers are available, we evaluate two common and a new genetic estimator of kinship. We show discrepancies between pedigree values and marker estimates of kinship and explore via simulations the possible reasons for these. We find these discrepancies are attributable to two main sources: pedigree errors and heterogeneity in the origin of founders. We also show that our new marker‐based kinship estimator has very good statistical properties and behaviour and is particularly well suited for situations where the source population is of small size, as will often be the case in conservation biology, and where high levels of kinship are expected, as is typical in social evolution studies.

Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass, Zostera marina

Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (FST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured "master" traits (like body size) might provide good predictions of overall trait differentiation.

Kinship influences sperm whale social organization within, but generally not among, social units

Sperm whales have a multi-level social structure based upon long-term, cooperative social units. What role kinship plays in structuring this society is poorly understood. We combined extensive association data (518 days, during 2005-2016) and genetic data (18 microsatellites and 346 bp mitochondrial DNA (mtDNA) control region sequences) for 65 individuals from 12 social units from the Eastern Caribbean to examine patterns of kinship and social behaviour. Social units were clearly matrilineally based, evidenced by greater relatedness within social units (mean r = 0.14) than between them (mean r = 0.00) and uniform mtDNA haplotypes within social units. Additionally, most individuals (82.5%) had a first-degree relative in their social unit, while we found no first-degree relatives between social units. Generally and within social units, individuals associated more with their closer relatives (matrix correlations: 0.18-0.25). However, excepting a highly related pair of social units that merged over the study period, associations between social units were not correlated with kinship (p > 0.1). These results are the first to robustly demonstrate kinship's contribution to social unit composition and association preferences, though they also reveal variability in association preferences that is unexplained by kinship. Comparisons with other matrilineal species highlight the range of possible matrilineal societies and how they can vary between and even within species.

Long-term group membership and dynamics in a wild western lowland gorilla population (Gorilla gorilla gorilla) inferred using non-invasive genetics

The social organization of a group-living animal is defined by a balance between group dynamic events such as group formation, group dissolution, and dispersal events and group stability in membership and over time. Understanding these processes, which are relevant for questions ranging from disease transmission patterns to the evolution of polygyny, requires long-term monitoring of multiple social units over time. Because all great ape species are long-lived and elusive, the number of studies on these key aspects of social organization are limited, especially for western lowland gorillas (Gorilla gorilla gorilla). In this study, we used non-invasive genetic samples collected within an approximately 100 km² area of Loango National Park, Gabon to reconstruct group compositions and changes in composition over more than a decade. We identified 98 gorillas and 11 mixed sex groups sampled during 2014-2017. Using published data from 85 individuals and 12 groups surveyed between 2005 and 2009 at the same locality, we tracked groups and individuals back in time. The identification of 11 silverbacks via parentage analyses and the genetic tracking of 39 individuals across studies allowed us to infer six group formations, five group dissolutions, and 40 dispersal events within 12 years. We also observed four groups persisting across the sampling periods with a maximum inferred existence of nearly 17 years and exhibiting variation in membership stability. Our results highlight the variation in composition and stability among groups of western lowland gorillas and illustrate the power of non-invasive genetic sampling for long-term monitoring.

Evaluating sample size to estimate genetic management metrics in the genomics era

Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations. We applied this approach to analyse empirical genomic data for 30 individuals from each of four different free-ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) populations in Montana and Wyoming, USA, through cross-species application of an Ovine array and analysis of approximately 14,000 single nucleotide polymorphisms (SNPs) after filtering. We examined intra- and interpopulation relationships using kinship and identity by state metrics, as well as FST between populations. By evaluating our simulation results, we concluded that a sample size of 25 was adequate for assessing these metrics using the Ovine array to genotype Rocky Mountain bighorn sheep herds. However, we conclude that a universal sample size rule may not be able to sufficiently address the complexities that impact genomic kinship and inbreeding estimates. Thus, we recommend that a pilot study and sample size simulation using R code we developed that includes empirical genotypes from a subset of populations of interest would be an effective approach to ensure rigour in estimating genomic kinship and population differentiation.

Female vervet monkeys fine-tune decisions on tolerance versus conflict in a communication network

Group living promotes opportunities for both cooperation and competition. Selection on the ability to cope with such opposing social opportunities has been proposed as a driving force in the evolution of large brains in primates and other social species. However, we still know little about the degree of complexity involved in such social strategies. Here, we report advanced social strategies in wild vervet monkeys. Building on recent experimental evidence that subordinate females trade grooming for tolerance from higher-ranking individuals during foraging activities, we show that the audience composition strongly affects this trade. First, tolerance was lower if the audience contained individuals that outranked the subordinate partner, independently of audience size and kinship relationships. Second, we found a significant interaction between previous grooming and relative rank of bystanders: dominant subjects valued recent grooming by subordinates while intermediate ranked subjects valued the option to aggress subordinate partners in the presence of a dominant audience. Aggressors were also more likely to emit coalition recruitment calls if the audience contained individuals that outranked the subordinate partner. In conclusion, vervet monkeys include both recent grooming and knowledge about third-party relationships to make complex decisions when trading grooming for tolerance, leading to a finely balanced trade-off between reciprocation and opportunities to reinforce rank relationships.

Sociodemographic factors modulate the spatial response of brown bears to vacancies created by hunting

There is a growing recognition of the importance of indirect effects from hunting on wildlife populations, e.g. social and behavioural changes due to harvest, which occur after the initial offtake. Nonetheless, little is known about how the removal of members of a population influences the spatial configuration of the survivors. We studied how surviving brown bears (Ursus arctos) used former home ranges that had belonged to casualties of the annual bear hunting season in southcentral Sweden (2007-2015). We used resource selection functions to explore the effects of the casualty's and survivor's sex, age and their pairwise genetic relatedness, population density and hunting intensity on survivors' spatial responses to vacated home ranges. We tested the competitive release hypothesis, whereby survivors that increase their use of a killed bear's home range are presumed to have been released from intraspecific competition. We found strong support for this hypothesis, as survivors of the same sex as the casualty consistently increased their use of its vacant home range. Patterns were less pronounced or absent when the survivor and casualty were of opposite sex. Genetic relatedness between the survivor and the casualty emerged as the most important factor explaining increased use of vacated male home ranges by males, with a stronger response from survivors of lower relatedness. Relatedness was also important for females, but it did not influence use following removal; female survivors used home ranges of higher related female casualties more, both before and after death. Spatial responses by survivors were further influenced by bear age, population density and hunting intensity. We have shown that survivors exhibit a spatial response to vacated home ranges caused by hunting casualties, even in nonterritorial species such as the brown bear. This spatial reorganization can have unintended consequences for population dynamics and interfere with management goals. Altogether, our results underscore the need to better understand the short- and long-term indirect effects of hunting on animal social structure and their resulting distribution in space.